
#######################################################
#                                                     #
#                        LGA                          #
#                  ---------------                    #
#                                                     #
#               Local-Global Alignment                #
#        A Method for Finding 3-D Similarities        #
#               in Protein Structures                 #
#                                                     #
#                  ------------ 10/2009               #
#                                                     #
#      Adam Zemla (adamz@llnl.gov)                    #
#      Lawrence Livermore National Laboratory, CA     #
#                                                     #
#######################################################

!!!   License for LGA program has expired  !!!
#   For updated version of the LGA program   #
# please contact Adam Zemla:  adamz@llnl.gov #

# Molecule1: number of CA atoms   43 (  356),  selected   43 , name one
# Molecule2: number of CA atoms   51 (  404),  selected   43 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:C  -ch2:C  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    43       7_C - 49_C        4.00     4.00
  LCS_AVERAGE:     84.31

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    18      32_C - 49_C        1.63     5.10
  LCS_AVERAGE:     26.90

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    16      34_C - 49_C        0.93     5.21
  LCS_AVERAGE:     20.11

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   43
LCS_GDT     RESIDUE       RESIDUE       SEGMENT_SIZE    GLOBAL DISTANCE TEST COLUMNS: number of residues under the threshold assigned to each residue pair
LCS_GDT   NAME NUMBER   NAME NUMBER    1.0  2.0  5.0    0.5  1.0  1.5  2.0  2.5  3.0  3.5  4.0  4.5  5.0  5.5  6.0  6.5  7.0  7.5  8.0  8.5  9.0  9.5 10.0
LCS_GDT     T     7_C     T     7_C      3   13   43      3    3    4    6   23   28   29   31   35   37   38   39   42   43   43   43   43   43   43   43 
LCS_GDT     K     8_C     K     8_C      4   13   43     12   16   19   24   26   28   29   31   35   37   38   39   42   43   43   43   43   43   43   43 
LCS_GDT     I     9_C     I     9_C      9   13   43      6    9   12   20   23   27   29   30   35   37   38   39   42   43   43   43   43   43   43   43 
LCS_GDT     L    10_C     L    10_C      9   13   43      6    9   15   22   26   28   29   31   35   37   38   39   42   43   43   43   43   43   43   43 
LCS_GDT     P    11_C     P    11_C      9   13   43      9   16   19   24   26   28   29   31   35   37   38   39   42   43   43   43   43   43   43   43 
LCS_GDT     C    12_C     C    12_C      9   13   43     12   16   19   24   26   28   29   31   35   37   38   39   42   43   43   43   43   43   43   43 
LCS_GDT     P    13_C     P    13_C      9   13   43     12   16   19   24   26   28   29   31   35   37   38   39   42   43   43   43   43   43   43   43 
LCS_GDT     R    14_C     R    14_C      9   13   43      6   10   19   24   26   28   29   31   35   37   38   39   42   43   43   43   43   43   43   43 
LCS_GDT     C    15_C     C    15_C      9   13   43      5   10   19   24   26   28   29   31   35   37   38   39   42   43   43   43   43   43   43   43 
LCS_GDT     N    16_C     N    16_C      9   13   43      5   10   19   24   26   28   29   31   35   37   38   39   42   43   43   43   43   43   43   43 
LCS_GDT     S    17_C     S    17_C      9   13   43      5   10   18   24   26   28   29   31   35   37   38   39   42   43   43   43   43   43   43   43 
LCS_GDT     M    18_C     M    18_C      9   13   43      5    6   10   24   26   28   29   31   35   37   38   39   42   43   43   43   43   43   43   43 
LCS_GDT     E    19_C     E    19_C      9   13   43      5    6   10   18   26   28   29   31   35   37   38   39   42   43   43   43   43   43   43   43 
LCS_GDT     T    20_C     T    20_C      6   13   43      3    4    5    6   11   17   25   29   35   37   38   39   42   43   43   43   43   43   43   43 
LCS_GDT     K    21_C     K    21_C      3   12   43      3    3    6   10   12   16   26   30   35   37   38   39   42   43   43   43   43   43   43   43 
LCS_GDT     F    22_C     F    22_C      3    6   43      3    3    4    5    6    7    7    9   10   16   36   38   42   43   43   43   43   43   43   43 
LCS_GDT     C    23_C     C    23_C      5    6   43      4    5    6    9   11   12   13   19   22   27   34   38   42   43   43   43   43   43   43   43 
LCS_GDT     Y    24_C     Y    24_C      5    6   43      4    5    6    9   11   12   13   17   22   27   34   38   42   43   43   43   43   43   43   43 
LCS_GDT     Y    25_C     Y    25_C      5    6   43      4    5    6    9   11   12   14   20   30   32   38   39   42   43   43   43   43   43   43   43 
LCS_GDT     N    26_C     N    26_C      5    6   43      4    5    5    8   11   12   16   20   32   37   38   39   42   43   43   43   43   43   43   43 
LCS_GDT     N    27_C     N    27_C      5    6   43      3    5    6    9   11   12   13   16   21   32   36   39   42   43   43   43   43   43   43   43 
LCS_GDT     Y    28_C     Y    28_C      7    9   43      3    6    7    8   12   14   18   27   35   37   38   39   42   43   43   43   43   43   43   43 
LCS_GDT     N    29_C     N    29_C      7    9   43      4    6    7   10   12   14   18   28   35   37   38   39   42   43   43   43   43   43   43   43 
LCS_GDT     V    30_C     V    30_C      7    9   43      4    6    7    9   12   20   27   31   35   37   38   39   42   43   43   43   43   43   43   43 
LCS_GDT     N    31_C     N    31_C      7    9   43      4    6    7    9   10   13   18   25   33   35   38   39   42   43   43   43   43   43   43   43 
LCS_GDT     Q    32_C     Q    32_C      7   18   43      4    6    7   12   17   25   29   31   35   37   38   39   42   43   43   43   43   43   43   43 
LCS_GDT     P    33_C     P    33_C      7   18   43      3    6   11   17   23   28   29   31   35   37   38   39   42   43   43   43   43   43   43   43 
LCS_GDT     R    34_C     R    34_C     16   18   43      5   16   19   24   26   28   29   31   35   37   38   39   42   43   43   43   43   43   43   43 
LCS_GDT     H    35_C     H    35_C     16   18   43     12   16   19   24   26   28   29   31   35   37   38   39   42   43   43   43   43   43   43   43 
LCS_GDT     F    36_C     F    36_C     16   18   43     12   16   19   24   26   28   29   31   35   37   38   39   42   43   43   43   43   43   43   43 
LCS_GDT     C    37_C     C    37_C     16   18   43     12   16   19   24   26   28   29   31   35   37   38   39   42   43   43   43   43   43   43   43 
LCS_GDT     K    38_C     K    38_C     16   18   43      9   16   19   24   26   28   29   31   34   37   38   39   42   43   43   43   43   43   43   43 
LCS_GDT     A    39_C     A    39_C     16   18   43     12   16   19   24   26   28   29   31   35   37   38   39   42   43   43   43   43   43   43   43 
LCS_GDT     C    40_C     C    40_C     16   18   43     12   16   19   24   26   28   29   31   35   37   38   39   42   43   43   43   43   43   43   43 
LCS_GDT     Q    41_C     Q    41_C     16   18   43      9   16   19   24   26   28   29   31   35   37   38   39   42   43   43   43   43   43   43   43 
LCS_GDT     R    42_C     R    42_C     16   18   43     12   16   19   24   26   28   29   31   35   37   38   39   42   43   43   43   43   43   43   43 
LCS_GDT     Y    43_C     Y    43_C     16   18   43     12   16   19   24   26   28   29   31   35   37   38   39   42   43   43   43   43   43   43   43 
LCS_GDT     W    44_C     W    44_C     16   18   43     12   16   19   24   26   28   29   31   35   37   38   39   42   43   43   43   43   43   43   43 
LCS_GDT     T    45_C     T    45_C     16   18   43     10   16   19   24   26   28   29   31   35   37   38   39   42   43   43   43   43   43   43   43 
LCS_GDT     S    46_C     S    46_C     16   18   43     12   16   19   24   26   28   29   31   35   37   38   39   42   43   43   43   43   43   43   43 
LCS_GDT     G    47_C     G    47_C     16   18   43      4   16   19   24   26   28   29   31   35   37   38   39   42   43   43   43   43   43   43   43 
LCS_GDT     G    48_C     G    48_C     16   18   43      4    9   18   24   26   28   29   31   35   37   38   39   42   43   43   43   43   43   43   43 
LCS_GDT     T    49_C     T    49_C     16   18   43      0    3   17   24   26   28   29   31   35   37   38   39   42   43   43   43   43   43   43   43 
LCS_AVERAGE  LCS_A:  43.78  (  20.11   26.90   84.31 )

GLOBAL_DISTANCE_TEST (summary information about detected largest sets of residues (represented by selected AToms) that can fit under specified thresholds)
GDT DIST_CUTOFF  0.50   1.00   1.50   2.00   2.50   3.00   3.50   4.00   4.50   5.00   5.50   6.00   6.50   7.00   7.50   8.00   8.50   9.00   9.50  10.00
GDT NUMBER_AT     12     16     19     24     26     28     29     31     35     37     38     39     42     43     43     43     43     43     43     43 
GDT PERCENT_AT  23.53  31.37  37.25  47.06  50.98  54.90  56.86  60.78  68.63  72.55  74.51  76.47  82.35  84.31  84.31  84.31  84.31  84.31  84.31  84.31
GDT RMS_LOCAL    0.37   0.51   0.80   1.21   1.36   1.60   1.70   2.30   3.01   3.18   3.32   3.43   3.90   4.00   4.00   4.00   4.00   4.00   4.00   4.00
GDT RMS_ALL_AT   5.78   5.71   5.70   5.38   5.29   5.10   5.16   4.60   4.17   4.13   4.09   4.09   4.01   4.00   4.00   4.00   4.00   4.00   4.00   4.00

# Checking swapping
#   possible swapping detected:  F    22_C      F    22_C
#   possible swapping detected:  Y    28_C      Y    28_C
#   possible swapping detected:  F    36_C      F    36_C
#   possible swapping detected:  Y    43_C      Y    43_C

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    T     7_C      T     7_C     4.147     0    0.668   0.547     7.618   36.905   27.075
LGA    K     8_C      K     8_C     2.018     4    0.530   0.520     4.487   54.167   33.122
LGA    I     9_C      I     9_C     3.964     0    0.114   1.529     5.884   53.810   40.060
LGA    L    10_C      L    10_C     2.902     0    0.028   0.129     5.280   59.524   46.310
LGA    P    11_C      P    11_C     0.379     0    0.109   0.193     1.559   92.976   86.871
LGA    C    12_C      C    12_C     0.611     0    0.027   0.144     0.993   92.857   95.238
LGA    P    13_C      P    13_C     1.679     0    0.181   0.378     2.322   75.000   72.925
LGA    R    14_C      R    14_C     2.249     0    0.156   0.832     6.335   63.095   48.139
LGA    C    15_C      C    15_C     2.209     0    0.174   0.890     2.486   70.833   71.587
LGA    N    16_C      N    16_C     1.715     0    0.066   0.805     4.435   72.857   65.536
LGA    S    17_C      S    17_C     1.813     0    0.037   0.520     2.167   68.810   74.683
LGA    M    18_C      M    18_C     2.329     0    0.089   0.694     3.423   64.762   59.226
LGA    E    19_C      E    19_C     2.711     4    0.242   0.249     3.275   53.571   31.005
LGA    T    20_C      T    20_C     4.920     0    0.608   1.421     8.328   46.190   30.408
LGA    K    21_C      K    21_C     5.253     0    0.664   1.029    10.359   21.667   14.339
LGA    F    22_C      F    22_C     8.989     0    0.642   1.345    18.624    3.929    1.429
LGA    C    23_C      C    23_C     9.307     0    0.590   0.873    10.810    1.190    0.873
LGA    Y    24_C      Y    24_C     9.121     0    0.080   0.200    10.068    5.595    3.968
LGA    Y    25_C      Y    25_C     7.840     0    0.023   0.216     9.539    3.810    7.738
LGA    N    26_C      N    26_C     8.215     0    0.132   0.678    10.065    5.952    4.821
LGA    N    27_C      N    27_C     9.910     0    0.064   0.123    14.199    0.595    0.298
LGA    Y    28_C      Y    28_C     8.734     0    0.324   1.379    10.501    2.500    2.024
LGA    N    29_C      N    29_C     7.832     0    0.080   0.336     9.494   13.452    8.036
LGA    V    30_C      V    30_C     6.138     0    0.024   1.171     8.503   16.429   14.150
LGA    N    31_C      N    31_C     7.902     0    0.092   0.382    13.569   10.119    5.119
LGA    Q    32_C      Q    32_C     4.205     0    0.065   0.956     5.379   42.619   41.693
LGA    P    33_C      P    33_C     2.536     0    0.109   0.169     4.474   59.286   51.633
LGA    R    34_C      R    34_C     1.331     0    0.189   1.385     5.574   81.548   64.675
LGA    H    35_C      H    35_C     1.673     0    0.101   1.295     6.320   72.857   54.905
LGA    F    36_C      F    36_C     1.511     0    0.017   0.424     3.031   79.286   68.052
LGA    C    37_C      C    37_C     1.177     0    0.024   0.195     1.874   77.143   81.587
LGA    K    38_C      K    38_C     2.191     0    0.067   0.915     4.820   66.786   56.349
LGA    A    39_C      A    39_C     1.997     0    0.038   0.034     1.997   72.857   72.857
LGA    C    40_C      C    40_C     1.381     0    0.048   0.068     1.678   79.286   84.603
LGA    Q    41_C      Q    41_C     1.827     0    0.019   0.059     2.807   72.857   65.820
LGA    R    42_C      R    42_C     1.107     0    0.040   1.265     7.131   85.952   61.039
LGA    Y    43_C      Y    43_C     1.038     0    0.014   1.385     9.329   81.429   50.794
LGA    W    44_C      W    44_C     1.081     0    0.071   0.550     4.635   81.429   61.293
LGA    T    45_C      T    45_C     1.577     0    0.041   0.071     1.659   77.143   76.531
LGA    S    46_C      S    46_C     2.284     0    0.621   0.815     4.869   54.524   59.444
LGA    G    47_C      G    47_C     1.497     0    0.068   0.068     1.497   81.429   81.429
LGA    G    48_C      G    48_C     1.438     0    0.712   0.712     3.682   69.762   69.762
LGA    T    49_C      T    49_C     1.366     0    0.048   0.109     5.801   62.857   49.592

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       43     172    172  100.00     348    348  100.00                51
SUMMARY(RMSD_GDC):     4.005          3.987                  5.067           44.895   39.158

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   43   51    4.0     31    2.30    55.882    50.861     1.294

LGA_LOCAL      RMSD:   2.296  Number of atoms:   31  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   4.597  Number of assigned atoms:   43 
Std_ASGN_ATOMS RMSD:   4.005  Standard rmsd on all 43 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.455860 * X  +  -0.691369 * Y  +  -0.560537 * Z  +  -5.139509
  Y_new =   0.857120 * X  +  -0.171273 * Y  +  -0.485809 * Z  +  -2.626531
  Z_new =   0.239868 * X  +  -0.701908 * Y  +   0.670662 * Z  +   7.677301 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  2.059598 -0.242230 -0.808159   [DEG:  118.0063  -13.8788  -46.3041 ]
ZXZ: -0.856695  0.835695  2.812298   [DEG:  -49.0850   47.8818  161.1328 ]
 
# END of job
